mtholder

#!/usr/bin/env
import sys

'''
python gen-curl-oti.py template.txt studies.txt
where studies.txt is the list of studies used in synthesis.
  and template is a cURL call with XYZ inplace of the study id (and no other XYZ)
cURL
'''

mtholder

#!/usr/bin/env python
import sys
import os
import json
import codecs
dn = sys.argv[1]
outfn = sys.argv[2]
d = {}
for s in os.listdir(dn):
  if s.endswith('.out'):

mtholder

#!/usr/bin/env python
from collections import defaultdict
import dendropy
import sys
import os
_SCRIPT_NAME = os.path.split(sys.argv[0])[-1]
def error(msg):
    sys.stderr.write('{}: Error: {}\n'.format(_SCRIPT_NAME, msg))

OUT = sys.stdout

mtholder

#!/bin/bash
echo 'This script installs the tools needed for propinquity as subdirectories'
echo 'of the working directory. This assumes that you have a C++ dev environment (g++, boost, automake, libtool)'
echo 'installed. See README files for propinquity and otcetera if those builds fail'
echo 'Also assumes virtualenv for python'

CONTEXT_DIR="${PWD}"
virtualenv propinquity-env
source propinquity-env/bin/activate

mtholder

#! /usr/bin/env python

import dendropy

def get_tree(r):
    tree_str = "((C:1.3,D:4.)34:0.034,(A:1.1,(B:1.2,X:1.6)26:0.026)12:0.0126,E:1.5);"
    tree = dendropy.Tree.get(
            data=tree_str,
            schema="newick",
            rooting=r,

mtholder

#!/usr/bin/env python
from __future__ import print_function
from peyotl.api import PhylesystemAPI
import sys
studyid = sys.argv[1]

phy = PhylesystemAPI(get_from='local')
nx = phy.get_study(studyid)['data']['nexml']
print(nx.keys())

mtholder

#!/bin/bash

cd ~
mkdir OpenTree
cd OpenTree/
git clone https://github.com/mtholder/propinquity.git

echo '[opentree]' > ~/.opentree
echo "home = $PWD" >> ~/.opentree
echo 'peyotl = %(home)s/peyotl' >> ~/.opentree

mtholder

#!/usr/bin/env python
import sys
try:
    annot_fp = sys.argv[1]
except:
    sys.exit("Expecting a path to an annotations.json file as the only argument.\n")
import json
import codecs
with codecs.open(annot_fp, 'rU', encoding='utf-8') as inp:
    obj = json.load(inp)

mtholder

\documentclass{article}
\usepackage{amsmath}
\usepackage{paralist}
\DeclareMathOperator*{\argmin}{argmin}
\begin{document}
\section*{Note on detecting whether a pattern is parsimony informative}
Let $\ell(T, c)$ be the unordered parsimony length of discrete character pattern $c$ on 
tree $T$ and $\ell(T, c, i)$ be the parsimony length that combination of pattern and tree
 when state $i$ is  enforced as the state for the root of the tree.
Data pattern $c$ is ``parsimony informative'' if and only if, 

mtholder

#!/bin/bash

# works on the unpacked dir that is posted under the link 
#    text "All pipeline outputs " on the release page.
# E.g. the release page https://tree.opentreeoflife.org/about/synthesis-release/v9.1
#    points to http://files.opentreeoflife.org/synthesis/opentree9.1/opentree9.1_output.tgz
#    as its versions of "All pipeline outputs"
#
# I downloaded that, unpacked it, and provide the path to that dir as the only
#    argument to this script.